Category Archives: Biochemistry

Biology Q&A’s

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This site is a great resource for VCE Biology students, allowing you to learn and review key concepts. The Biochemistry section has seven areas of study including:

If you are a Twitter user, you can follow BiologyQuestions for regular questions and links about Biology topics. This site has over 17 thousand followers from across the world, so you will be part of a global community!

Week 2: Proteins


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Proteins are polypeptides or chains of peptides (amino acids) joined together by peptide bonds. These large organic molecules have four levels of structure –

  1. Primary – order of amino acids in the chain
  2. Secondary – alpha-helices, beta-pleats and random coils
  3. Tertiary – the folding of the chains due to the presence of disulphide bonds
  4. Quarternary – when two or more polypeptide chains are folded together in a complex molecule

Enzymes are a specific type of protein that play a critically important role in living organisms. The molecules in cells are constantly interacting – being broken down, built up or exchanged. These chemical reactions constitute an organism’s metabolism. An organism is regulated and the rate of it’s chemical activity is maintained by these special proteins, known as biological catalysts. Like all proteins, enzymes are made in the ribosomes by linking together specific amino acids in the cytoplasm, according to the DNA code. Each cell contains and needs a very large number of different enzymes, but not all cells produce all enzymes – it depends on the structure and function of the cell as to which genes are ‘switched on’.

  • Enzymes are proteins and are therefore made up of amino acids (containing carbon, hydrogen, oxygen and nitrogen)
  • Enzymes are ‘biological catalysts’ because they speed up the rate of a chemical reaction
  • Enzymes remain unchanged at the end of the reaction (not used up)
  • Enzymes are only required in small amounts
  • Enzymes are highly specific (one enzyme catalyses one type of reaction)
  • Enzymes work best under optimum conditions of temperature and acidity
  • Enzymes are ‘denatured’ (destroyed) by heat and sensitive to pH
  • Enzymes work like a key fits into a lock – their shape complements the shape of the substrate materials.
  • The ‘active site’ of a particular enzyme has a specific shape into which only one kind of substrate will fit
  • Enzymes may need ‘co-enzymes’ (specific vitamins) or ‘co-factors’  (minerals) to help functioning

Week 1: Biomacromolecules

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During our “step-up” program we studied the four different types of biological macromolecules, known as:

  • Carbohydrates (or saccharides) made up of glucose monomers
  • Lipids made up of fatty acids and glycerol
  • Proteins (or polypeptides) made up of amino acids
  • Nucleic acids (DNA and RNA) made up of nucleic acids

We investigated how these molecules are built up through condensation reactions, in which water is released. Hydrolysis reactions occur when these molecules are broken down with the addition of water.

Photosynthesis by video conference from GTAC

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GTAC – Introduction to Photosynthesis on YouTube

GTAC – Photosynthesis – Light Dependent Cycle and an Animation showing six cycles of the Light Independent Cycle on YouTube

Tony, from GTAC, demonstrated a photosynthesis experiment in which equal quantities of spinach leaves were placed in four clear, closed containers. Each container was subjected to light of the same intensity, but one had no filter (control) and the other three were wrapped in coloured cellophane (red, blue and green, as shown above). The coloured cellophane filters out different wavelengths of light, so the red cellophane reflects red wavelengths and allows other wavelengths to pass through. Each container had two probes, measuring oxygen and carbon dioxide concentrations in parts per million (ppm). What would you expect to happen in the cellophane-covered containers compared to the control?

Tony was also able to answer two questions that students have about DNA transcription.

(1) Where does the mRNA molecule go after transcription? “A single mRNA can be translated many times by ribosomes into polypeptides (it’s one way a cellular response dependent on gene expression can be amplified).  After that mRNA is degraded, releasing individual nucleotides which can then be recycled into new mRNA.  In eukaryotic cells, the mRNA is protected by the 5’ methylguanosine cap and the 3’ poly-A tail.  When these are removed from the ends, presumably in response to an intracellular signal that says the mRNA is no longer required, the mRNA becomes susceptible to degradation.”

 (2) When and where does transcription occur? “I would say transcription (the process by which the mRNA is first made from DNA template) occurs in the nucleus of eukaryotic cells almost continuously but the genes being expressed change throughout the cell cycle and in response to stimuli.  For example, genes relevant to growth may be transcribed during G phases.  A special set of genes relevant to DNA synthesis are transcribed during S phase.  If a (stem) cell received a differentiation signal, a relevant set of genes would be switched on for differentiation into a particular cell type.  I would say the only time transcription ceases is when the chromosomes condense for mitosis and cytokinesis.  Essential proteins are still around to ensure cell division proceeds as intended.  After cell division and the chromosomes de-condense, it’s back to business as usual.”

Thanks Tony for these valuable extensions to our Year 12 Biology program at Hawkesdale P12 College.

Cupcake mitosis


Students in Year 11 Biology are learning the phases of mitosis, so we baked and decorated these cupcakes. Students now have a good understanding of what happens inside the nucleus during:

  • Interphase
  • Prophase
  • Metaphase
  • Anaphase
  • Telophase and
  • Cytokinesis.

Watch the Cells Alive Interactive and describe where in each cycle are the three checkpoints that allow DNA replication and mitosis to continue. Why is it incorrect to suggest that the cell is “resting” during interphase, between mitotic cycles?

Photosynthesis and Respiration

Photosynthesis and cellular respiration are ‘opposite’ reactions in the carbon cycle – one is endothermic (requires the input of energy) and one is exothermic (releases energy). Once you have read Chapter 3 and answered the chapter review questions, watch these videos and test your understanding by completing the “Photosynthesis/Respiration” worksheet. Whereas photosynthesis occurs only in the chloroplasts of plants, cellular respiration occurs in the mitochondria of both plants, fungi and animals. You will need to know these biochemical processes in a good deal of detail for the exam.

Exploring Protein Structure with GTAC

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The Gene Technology Access Centre have some excellent resources for VCE Biology, including this slideshow and activity sheets “exploring protein structure“.  The image above is one view of a representation of the enzyme amylase, which breaks starch down into sugars. You can see the green alpha-helices, yellow beta-sheets and blue random coils in the secondary structure of this protein. You may also be able to see the ‘co-factors’ or molecules which assist at the active site of this enzyme. Amylase relies on the co-factors calcium and chloride to function efficiently. What are the dietary sources of calcium and chloride?

View the GTAC Bioinformatics Task 4 Presentation and then complete student worksheets #1 and #2. You will need to download the Cn3D software to view the interactive protein molecules.


Recombinant DNA technologies


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On Monday we had the opportunity to connect with the Gene Technology Access Centre via the video conferencing equipment, Polycom. Nicole and Frazer facilitated a great session about recombinant DNA technology, including a demonstration of gel electrophoresis to determine if genes had been successfully inserted into a plasmid.

Did you know that humans have the same gene sequences as other organisms?

  • 61% similarity to fruit flies
  • 99% similarity to mice
  • 99.9% similarity to chimpanzees

The human genome has 22 pairs of autosomes and 1 pair of sex chromosomes (XX in females and XY in males). Chromosomes exisit in the nucleus (as single strands) and there is also some (maternal – passed down from the mother) DNA in the mitochondria, which is circular. Prokatyotes (bacteria) also have circular DNA called ‘plasmids’.

Sea jellies have a gene that codes for a protein that is luminescent, called a “green fluorescent protein”. This gene is a useful marker, to determine if other genes have been successfully introduced to an organism.

Restriction enzymes (used for ‘cutting’ DNA) are used to open the plasmid, the new gene is inserted and then a DNA ligase is used to stick the ends together. We are using four different restriction enzymes (EcoRY13; BamH1; Nhe1 and Sma1). The DNA sequence at a restriction site is a palindrome – reads the same forwards and backwards. Some restriction enzymes cause ‘sticky’ ends (uneven or with a tail – exposed base pairs) while others cause ‘blunt’ ends (no overhanging base pairs). Once the new gene is inserted, complementary base pairs are joined by hydrogen bonds – or ‘pasted together’ with DNA ligase.

This is the process we will model using the paper cut-outs:

  1. E.coli is a bacteria that can be resistant to various antibiotics (eg. Amp R = ampicillin resistant).
  2. Cut the plasmid using a restriction enzyme.
  3. Insert the gene of interest into the plasmid, stick it together and produce the recombinant plasmid, which should contain the ampicillin resistance gene as well as the “GFP” (green fluorescent protein) gene.
  4. To test if the recombination has been successful, we need to use the restriction enzymes to produce various lengths of DNA. These are then pipetted into ‘wells’ in the gel. Because DNA is a negatively charged molecule, we load the wells at the negative end and attach the positive wire to the other end, so that the pieces of DNA a drawn through the gel matrix to the other side. The longest pieces move more slowly and travel the shortest distance, while the shortest molecules move most quickly through the gel and travel the greatest distance.



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To survive, every multicelluar organism needs a way for cells in one part of the organism to ‘know’ what cells in another part of the organism are doing. If you think about the human body as a population, with each cell an individual person, the endocrine and nervous systems

Signalling molecules are chemical compounds that receive and transmit messages around an organism. These can include simple ‘neurotransmitters’ of the nervous system, or larger hormones (protein compounds) of the endocrine system.

  1. What is a neurotransmitters?
  2. What four criteria must be met to be classified as a neurotransmitter?
  3. What are the four steps in neurotransmission?
  4. There are two main types of neurotransmitters – Large peptides and smaller amino acids and amines. Draw up a table showing examples of each and briefly describe how they function. For example, dopamine influences the mood and behaviour.